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Uncertainty quantification is an important prerequisite for the deployment of deep learning models in safety-critical areas. Yet, this hinges on the uncertainty estimates being useful to the extent the prediction intervals are well-calibrated and sharp. In the absence of inherent uncertainty estimates (e.g. pretrained models predicting only point estimates), popular approaches that operate post-hoc include Laplace’s method and split conformal prediction (split-CP). However, Laplace’s method can be miscalibrated when the model is misspecified and split-CP requires sample splitting, and thus comes at the expense of statistical efficiency. In this work, we construct prediction intervals for neural network regressors post-hoc without held-out data. This is achieved by approximating the full conformal prediction method (full-CP). Whilst full-CP nominally requires retraining the model for every test point and candidate label, we propose to train just once and locally perturb model parameters using Gauss-Newton influence to approximate the effect of retraining. Coupled with linearization of the network, we express the absolute residual nonconformity score as a piecewise linear function of the candidate label allowing for an efficient procedure that avoids the exhaustive search over the output space. On standard regression benchmarks and bounding box localization, we show the resulting prediction intervals are locally-adaptive and often tighter than those of split-CP.

This paper investigates whether sequence models can learn to perform numerical algorithms, e.g. gradient descent, on the fundamental problem of least squares. Our goal is to inherit two properties of standard algorithms from numerical analysis: (1) machine precision, i.e. we want to obtain solutions that are accurate to near floating point error, and (2) numerical generality, i.e. we want them to apply broadly across problem instances. We find that prior approaches using Transformers fail to meet these criteria, and identify limitations present in existing architectures and training procedures. First, we show that softmax Transformers struggle to perform high-precision multiplications, which prevents them from precisely learning numerical algorithms. Second, we identify an alternate class of architectures, comprised entirely of polynomials, that can efficiently represent high-precision gradient descent iterates. Finally, we investigate precision bottlenecks during training and address them via a high-precision training recipe that reduces stochastic gradient noise. Our recipe enables us to train two polynomial architectures, gated convolutions and linear attention, to perform gradient descent iterates on least squares problems. For the first time, we demonstrate the ability to train to near machine precision. Applied iteratively, our models obtain $100,000\times$ lower MSE than standard Transformers trained end-to-end and they incur a $10,000\times$ smaller generalization gap on out-of-distribution problems. We make progress towards end-to-end learning of numerical algorithms for least squares.

In the analysis of brain functional MRI (fMRI) data using regression models, Bayesian methods are highly valued for their flexibility and ability to quantify uncertainty. However, these methods face computational challenges in high-dimensional settings typical of brain imaging, and the often pre-specified correlation structures may not accurately capture the true spatial relationships within the brain. To address these issues, we develop a general prior specifically designed for regression models with large-scale imaging data. We introduce the Soft-Thresholded Conditional AutoRegressive (ST-CAR) prior, which reduces instability to pre-fixed correlation structures and provides inclusion probabilities to account for the uncertainty in choosing active voxels in the brain. We apply the ST-CAR prior to scalar-on-image (SonI) and image-on-scalar (IonS) regression models—both critical in brain imaging studies—and develop efficient computational algorithms using variational inference (VI) and stochastic subsampling techniques. Simulation studies demonstrate that the ST-CAR prior outperforms existing methods in identifying active brain regions with complex correlation patterns, while our VI algorithms offer superior computational performance. We further validate our approach by applying the ST-CAR to working memory fMRI data from the Adolescent Brain Cognitive Development (ABCD) study, highlighting its effectiveness in practical brain imaging applications.

Quantifying uncertainty is an essential part of predictive modeling, especially in the context of high-stakes decision-making. While classification output includes data uncertainty by design in the form of class probabilities, the regression task generally aims only to predict the expected value of the target variable. Probabilistic extensions often assume parametric distributions around the expected value, optimizing the likelihood over the resulting explicit densities. However, using parametric distributions can limit practical applicability, making it difficult for models to capture skewed, multi-modal, or otherwise complex distributions. In this paper, we propose optimizing a novel nondeterministic neural network regression architecture for loss functions derived from a sample-based approximation of the continuous ranked probability score (CRPS), enabling a truly distribution-free approach by learning to sample from the target's aleatoric distribution, rather than predicting explicit densities. Our approach allows the model to learn well-calibrated, arbitrary uni- and multivariate output distributions. We evaluate the method on a variety of synthetic and real-world tasks, including uni- and multivariate problems, function inverse approximation, and standard regression uncertainty benchmarks. Finally, we make all experiment code publicly available.

Modeling kinetic equations is essential for understanding the mechanisms of chemical reactions, yet a complex and time-consuming task. Kinetic equation prediction is formulated as a problem of dynamical symbolic regression (DSR) subject to physical chemistry constraints. Deep learning (DL) holds the potential to capture reaction patterns and predict kinetic equations from data of chemical species, effectively avoiding empirical bias and improving efficiency compared with traditional analytical methods. Despite numerous studies focusing on DSR and the introduction of Transformers to predict ordinary differential equations, the corresponding models lack generalization abilities across diverse categories of reactions. In this study, we propose KinFormer, a generalizable kinetic equation prediction model. KinFormer utilizes a conditional Transformer to model DSR under physical constraints and employs Monte Carlo Tree Search to apply the model to new types of reactions. Experimental results on 20 types of organic reactions demonstrate that KinFormer not only outperforms classical baselines, but also exceeds Transformer baselines in out-of-domain evaluations, thereby proving its generalization ability.

Mathematical equations have been unreasonably effective in describing complex natural phenomena across various scientific disciplines. However, discovering such insightful equations from data presents significant challenges due to the necessity of navigating extremely large combinatorial hypothesis spaces. Current methods of equation discovery, commonly known as symbolic regression techniques, largely focus on extracting equations from data alone, often neglecting the domain-specific prior knowledge that scientists typically depend on. They also employ limited representations such as expression trees, constraining the search space and expressiveness of equations. To bridge this gap, we introduce LLM-SR, a novel approach that leverages the extensive scientific knowledge and robust code generation capabilities of Large Language Models (LLMs) to discover scientific equations from data. Specifically, LLM-SR treats equations as programs with mathematical operators and combines LLMs' scientific priors with evolutionary search over equation programs. The LLM iteratively proposes new equation skeleton hypotheses, drawing from its domain knowledge, which are then optimized against data to estimate parameters. We evaluate LLM-SR on four benchmark problems across diverse scientific domains (e.g., physics, biology), which we carefully designed to simulate the discovery process and prevent LLM recitation. Our results demonstrate that LLM-SR discovers physically accurate equations that significantly outperform state-of-the-art symbolic regression baselines, particularly in out-of-domain test settings. We also show that LLM-SR's incorporation of scientific priors enables more efficient equation space exploration than the baselines.

Symbolic regression, a task discovering the formula best fitting the given data, is typically based on the heuristical search. These methods usually update candidate formulas to obtain new ones with lower prediction errors iteratively. However, since formulas with similar function shapes may have completely different symbolic forms, the prediction error does not decrease monotonously as the search approaches the target formula, causing the low recovery rate of existing methods. To solve this problem, we propose a novel search objective based on the minimum description length, which reflects the distance from the target and decreases monotonically as the search approaches the correct form of the target formula. To estimate the minimum description length of any input data, we design a neural network, MDLformer, which enables robust and scalable estimation through large-scale training. With the MDLformer's output as the search objective, we implement a symbolic regression method, SR4MDL, that can effectively recover the correct mathematical form of the formula. Extensive experiments illustrate its excellent performance in recovering formulas from data. Our method successfully recovers around 50 formulas across two benchmark datasets comprising 133 problems, outperforming state-of-the-art methods by 43.92%. Experiments on 122 unseen black-box problems further demonstrate its generalization performance. We release our code at https://github.com/tsinghua-fib-lab/SR4MDL .

Data-driven modeling of dynamical systems is a crucial area of machine learning. In many scenarios, a thorough understanding of the model’s behavior becomes essential for practical applications. For instance, understanding the behavior of a pharmacokinetic model, constructed as part of drug development, may allow us to both verify its biological plausibility (e.g., the drug concentration curve is non-negative and decays to zero in the long term) and to design dosing guidelines (e.g., by looking at the peak concentration and its timing). Discovery of closed-form ordinary differential equations (ODEs) can be employed to obtain such insights by finding a compact mathematical equation and then analyzing it (a two-step approach). However, its widespread use is currently hindered because the analysis process may be time-consuming, requiring substantial mathematical expertise, or even impossible if the equation is too complex. Moreover, if the found equation's behavior does not satisfy the requirements, editing it or influencing the discovery algorithms to rectify it is challenging as the link between the symbolic form of an ODE and its behavior can be elusive. This paper proposes a conceptual shift to modeling low-dimensional dynamical systems by departing from the traditional two-step modeling process. Instead of first discovering a closed-form equation and then analyzing it, our approach, direct semantic modeling, predicts the semantic representation of the dynamical system (i.e., description of its behavior) directly from data, bypassing the need for complex post-hoc analysis. This direct approach also allows the incorporation of intuitive inductive biases into the optimization algorithm and editing the model's behavior directly, ensuring that the model meets the desired specifications. Our approach not only simplifies the modeling pipeline but also enhances the transparency and flexibility of the resulting models compared to traditional closed-form ODEs.

The active regression problem of the single-index model is to solve $\min_x \lVert f(Ax)-b\rVert_p$, where $A$ is fully accessible and $b$ can only be accessed via entry queries, with the goal of minimizing the number of queries to the entries of $b$. When $f$ is Lipschitz, previous results only obtain constant-factor approximations. This work presents the first algorithm that provides a $(1+\varepsilon)$-approximation solution by querying $\tilde{O}(d^{\frac{p}{2}\vee 1}/\varepsilon^{p\vee 2})$ entries of $b$. This query complexity is also shown to be optimal up to logarithmic factors for $p\in [1,2]$ and the $\varepsilon$-dependence of $1/\varepsilon^p$ is shown to be optimal for $p>2$.

For deep regression, preserving the ordinality of the targets with respect to the feature representation improves performance across various tasks. However, a theoretical explanation for the benefits of ordinality is still lacking. This work reveals that preserving ordinality reduces the conditional entropy $H(Z|Y)$ of representation $Z$ conditional on the target $Y$. However, our findings reveal that typical regression losses fail to sufficiently reduce $H(Z|Y)$, despite its crucial role in generalization performance. With this motivation, we introduce an optimal transport-based regularizer to preserve the similarity relationships of targets in the feature space to reduce $H(Z|Y)$. Additionally, we introduce a simple yet efficient strategy of duplicating the regressor targets, also with the aim of reducing $H(Z|Y)$. Experiments on three real-world regression tasks verify the effectiveness of our strategies to improve deep regression. Code: https://github.com/needylove/Regression_tightness

Against the backdrop of enthusiasm for large language models (LLMs), there is a growing need to scientifically assess their capabilities and shortcomings. This is nontrivial in part because it is difficult to find tasks which the models have not encountered during training. Utilizing symbolic graphics programs, we propose a domain well-suited to test multiple spatial-semantic reasoning skills of LLMs. Popular in computer graphics, these programs procedurally generate visual data. While LLMs exhibit impressive skills in general program synthesis and analysis, symbolic graphics programs offer a new layer of evaluation: they allow us to test an LLM's ability to answer semantic questions about the images or 3D geometries without a vision encoder. To semantically understand the symbolic programs, LLMs would need to possess the ability to "imagine" and reason how the corresponding graphics content would look with only the symbolic description of the local curvatures and strokes. We use this task to evaluate LLMs by creating a large benchmark for the semantic visual understanding of symbolic graphics programs, built procedurally with minimal human effort. Particular emphasis is placed on transformations of images that leave the image level semantics invariant while introducing significant changes to the underlying program. We evaluate commercial and open-source LLMs on our benchmark to assess their ability to reason about visual output of programs, finding that LLMs considered stronger at reasoning generally perform better. Lastly, we introduce a novel method to improve this ability -- Symbolic Instruction Tuning (SIT), in which the LLM is finetuned with pre-collected instruction data on symbolic graphics programs. Interestingly, we find that SIT not only improves LLM's understanding on symbolic programs, but it also improves general reasoning ability on various other benchmarks.

Discovering group structures within data poses a fundamental challenge across diverse scientific domains. A key obstacle is the non-differentiable nature of group axioms, hindering their integration into deep learning frameworks. To address this, we introduce a novel differentiable approach leveraging the representation theory of finite groups. Our method features a unique network architecture that models interactions between group elements via matrix multiplication of their representations, along with a regularizer promoting the unitarity of these representations. The interplay between the network architecture and the unitarity condition implicitly encourages the emergence of valid group structures. Evaluations demonstrate our method's ability to accurately recover group operations and their unitary representations from partial observations, achieving significant improvements in sample efficiency and a $\times 1000$ speedup over the state of the art. This work lays the foundation for a promising new paradigm in automated algebraic structure discovery, with potential applications across various domains, including automatic symmetry discovery for geometric deep learning.

We explore the capability of transformers to address endogeneity in in-context linear regression. Our main finding is that transformers inherently possess a mechanism to handle endogeneity effectively using instrumental variables (IV). First, we demonstrate that the transformer architecture can emulate a gradient-based bi-level optimization procedure that converges to the widely used two-stage least squares (2SLS) solution at an exponential rate. Next, we propose an in-context pretraining scheme and provide theoretical guarantees showing that the global minimizer of the pre-training loss achieves a small excess loss. Our extensive experiments validate these theoretical findings, showing that the trained transformer provides more robust and reliable in-context predictions and coefficient estimates than the 2SLS method, in the presence of endogeneity.

Deep neural networks based on state space models (SSMs) are attracting significant attention in sequence modeling since their computational cost is much smaller than that of Transformers. While the capabilities of SSMs have been demonstrated through experiments in various tasks, theoretical understanding of SSMs is still limited. In particular, most theoretical studies discuss the capabilities of SSM layers without nonlinear layers, and there is a lack of discussion on their combination with nonlinear layers. In this paper, we explore the capabilities of SSMs combined with fully connected neural networks, and show that they are comparable to Transformers in extracting the essential tokens depending on the input. As concrete examples, we consider two synthetic tasks, which are challenging for a single SSM layer, and demonstrate that SSMs combined with nonlinear layers can efficiently solve these tasks. Furthermore, we study the nonparametric regression task, and prove that the ability of SSMs is equivalent to that of Transformers in estimating functions belonging to a certain class.

Spatiotemporal dynamics pervade the natural sciences, from the morphogen dynamics underlying patterning in animal pigmentation to the protein waves controlling cell division. A central challenge lies in understanding how controllable parameters induce qualitative changes in system behavior called bifurcations. This endeavor is particularly difficult in realistic settings where governing partial differential equations (PDEs) are unknown and data is limited and noisy. To address this challenge, we propose TRENDy (Temporal Regression of Effective Nonlinear Dynamics), an equation-free approach to learning low-dimensional, predictive models of spatiotemporal dynamics. TRENDy first maps input data to a low-dimensional space of effective dynamics through a cascade of multiscale filtering operations. Our key insight is the recognition that these effective dynamics can be fit by a neural ordinary differential equation (NODE) having the same parameter space as the input PDE. The preceding filtering operations strongly regularize the phase space of the NODE, making TRENDy significantly more robust to noise compared to existing methods. We train TRENDy to predict the effective dynamics of synthetic and real data representing dynamics from across the physical and life sciences. We then demonstrate how we can automatically locate both Turing and Hopf bifurcations in unseen regions of parameter space. We finally apply our method to the analysis of spatial patterning of the ocellated lizard through development. We found that TRENDy's predicted effective state not only accurately predicts spatial changes over time but also identifies distinct pattern features unique to different anatomical regions, such as the tail, neck, and body--an insight that highlights the potential influence of surface geometry on reaction-diffusion mechanisms and their role in driving spatially varying pattern dynamics.

Symbolic regression is a key task in machine learning, aiming to discover mathematical expressions that best describe a dataset. While deep learning has increased interest in using neural networks for symbolic regression, many existing approaches rely on pre-trained models. These models require significant computational resources and struggle with regression tasks involving unseen functions and variables. A pre-training-free paradigm is needed to better integrate with search-based symbolic regression algorithms. To address these limitations, we propose a novel framework for symbolic regression that integrates evolutionary feature construction with a neural network, without the need for pre-training. Our approach adaptively generates symbolic trees that align with the desired semantics in real-time using a language model trained via online supervised learning, providing effective building blocks for feature construction. To mitigate hallucinations from the language model, we design a retrieval-augmented generation mechanism that explicitly leverages searched symbolic expressions. Additionally, we introduce a scale-invariant data augmentation technique that further improves the robustness and generalization of the model. Experimental results demonstrate that our framework achieves state-of-the-art accuracy across 25 regression algorithms and 120 regression tasks.

We examine the implicit bias of mirror flow in least squares error regression with wide and shallow neural networks. For a broad class of potential functions, we show that mirror flow exhibits lazy training and has the same implicit bias as ordinary gradient flow when the network width tends to infinity. For univariate ReLU networks, we characterize this bias through a variational problem in function space. Our analysis includes prior results for ordinary gradient flow as a special case and lifts limitations which required either an intractable adjustment of the training data or networks with skip connections. We further introduce \emph{scaled potentials} and show that for these, mirror flow still exhibits lazy training but is not in the kernel regime. For univariate networks with absolute value activations, we show that mirror flow with scaled potentials induces a rich class of biases, which generally cannot be captured by an RKHS norm. A takeaway is that whereas the parameter initialization determines how strongly the curvature of the learned function is penalized at different locations of the input space, the scaled potential determines how the different magnitudes of the curvature are penalized.

The efficiency of Logic Optimization (LO) has become one of the key bottlenecks in chip design. To prompt efficient LO, previous studies propose using a key scoring function to predict and prune a large number of ineffective nodes of the LO heuristics. However, the existing scoring functions struggle to balance inference efficiency, interpretability, and generalization performance, which severely hinders their application to modern LO tools. To address this challenge, we propose a novel data-driven circuit symbolic learning framework, namely CMO, to learn lightweight, interpretable, and generalizable scoring functions. The major challenge of developing CMO is to discover symbolic functions that can well generalize to unseen circuits, i.e., the circuit symbolic generalization problem. Thus, the major technical contribution of CMO is the novel Graph Enhanced Symbolic Discovery framework, which distills dark knowledge from a well-designed Graph Neural Network (GNN) to enhance the generalization capability of the learned symbolic functions. To the best of our knowledge, CMO is *the first* graph-enhanced approach for discovering lightweight and interpretable symbolic functions that can well generalize to unseen circuits in LO. Experiments on three challenging circuit benchmarks show that the *interpretable* symbolic functions learned by CMO outperform previous state-of-the-art (SOTA) GPU-based and human-designed approaches in terms of *inference efficiency* and *generalization capability*. Moreover, we integrate CMO with the Mfs2 heuristic---one of the most time-consuming LO heuristics. The empirical results demonstrate that CMO significantly improves its efficiency while keeping comparable optimization performance when executed on a CPU-based machine, achieving up to 2.5× faster runtime.

Attention-based models, such as Transformer, excel across various tasks but lack a comprehensive theoretical understanding, especially regarding token-wise sparsity and internal linear representations. To address this gap, we introduce the single-location regression task, where only one token in a sequence determines the output, and its position is a latent random variable, retrievable via a linear projection of the input. To solve this task, we propose a dedicated predictor, which turns out to be a simplified version of a non-linear self-attention layer. We study its theoretical properties, by showing its asymptotic Bayes optimality and analyzing its training dynamics. In particular, despite the non-convex nature of the problem, the predictor effectively learns the underlying structure. This work highlights the capacity of attention mechanisms to handle sparse token information and internal linear structures.

The problem of symbolic regression (SR) arises in many different applications, such as identifying physical laws or deriving mathematical equations describing the behavior of financial markets from given data. Various methods exist to address the problem of SR, often based on genetic programming. However, these methods are usually complicated and involve various hyperparameters. In this paper, we present our new approach ParFam that utilizes parametric families of suitable symbolic functions to translate the discrete symbolic regression problem into a continuous one, resulting in a more straightforward setup compared to current state-of-the-art methods. In combination with a global optimizer, this approach results in a highly effective method to tackle the problem of SR. We theoretically analyze the expressivity of ParFam and demonstrate its performance with extensive numerical experiments based on the common SR benchmark suit SRBench, showing that we achieve state-of-the-art results. Moreover, we present an extension incorporating a pre-trained transformer network (DL-ParFam) to guide ParFam, accelerating the optimization process by up to two magnitudes. Our code and results can be found at https://github.com/Philipp238/parfam.